covid-19... toll-free number 0800 029 999 page 1 south africa week 46 2020covid-19 testing summary...

TOLL-FREE NUMBER 0800 029 999 PAGE 1www.nicd.ac.za

S O U T H A F R I C A W E E K 4 6 2 0 2 0

COVID-19 TESTING SUMMARY

• In the period 1 March 2020 through 14 November 2020, 4,354,676 laboratory tests for SARS-CoV-2 have been conducted nationally

• Weekly testing volumes have decreased since a peak in week 28. The number of tests performed in week 46 were similar to the previous few weeks

• Western Cape (275 per 100,000 persons), Eastern Cape (248 per 100,000 persons), Northern Cape (233 per 100,000 persons) and Free State (230 per 100,000 persons) provinces had the highest testing rates in week 46

• Percentage testing positive has decreased since the peak of 31.2% in week 29. In week 46 the percentage testing positive was 11.0%, slightly higher than the previous six weeks

• Percentage testing positive was highest in the Eastern Cape (31.9%) and Western Cape (12.2%). Percentages testing positive were <10% in Northern Cape, Free State, North West, Gauteng, KwaZulu-Natal, Mpumalanga and Limpopo.

• In week 46, compared to the previous week, the percentage testing positive increased in the Eastern Cape and Western Cape, decreased in Northern Cape, Free State, and Mpumalanga, and did not change in KwaZulu-Natal, North West, Gauteng and Limpopo

• Mean laboratory turnaround time in week 46 was 1.4 days; 1.9 days in the public sector and 1.0 days in the private sector

This report summarises national laboratory testing for SARS-CoV-2, the virus causing COVID-19, in South Africa. This report is based on data for specimens reported up to 14 November 2020 (Week 46 of 2020).

OVERVIEW OF REPORT

HIGHLIGHTS




Methods

Testing for SARS-CoV-2 began on 28 January 2020 at the NICD and after the first case was confirmed on 5th March 2020, testing was expanded to a larger network of private and NHLS laboratories. Laboratory testing was conducted for people meeting the case definition for persons under investigation (PUI). This definition was updated several times over the reporting period but at different times included (i) symptomatic individuals seeking testing, (ii) hospitalized individuals for whom testing was done, (iii) individuals in high-risk occupations, (iv) individuals in outbreak settings, and (v) individuals identified through community screening and testing (CST) programmes which were implemented in April 2020 and was discontinued from the week beginning 17th May. CST was implemented differently in different provinces, and ranged from mass screening approaches (including asymptomatic individuals) to screening of individuals in contact with a confirmed case to targeted testing of clusters of cases. Respiratory specimens were submitted to testing laboratories. Testing was performed using reverse transcriptase real-time PCR, which detects SARS-CoV-2 viral genetic material. Laboratories used any one of several in-house and commercial PCR assays to test for the presence of SARS-CoV-2 RNA. Test results were automatically fed into a data warehouse after result authorisation. We excluded specimens collected outside South Africa and duplicate test results for an individual. Date of specimen receipt in the laboratory was used when date of specimen collection was missing. Proportion testing positive (PTP) was calculated as the number of positive tests/total number of tests and presented as percentage by multiplying with 100. We used 2020 mid-year population estimates from Statistics South Africa to calculate the testing rate, expressed as tests per 100 000 persons. Patient admission status was determined for public sector tests based on the reported patient facility. Laboratory turnaround times were calculated as the mean number of days between specimen collection and reporting of the result. Categorical variables were compared using

the chi-squared test, and continuous variables with the students t-test, with a P-value<0.05 considered statistically significant.

Health district and sub-district level results included only public sector data, and were mapped based on the testing facility. Estimates of overall prevalence were derived using regression techniques. Estimates were adjusted to produce district-specific positive test prevalence based on the average age profile, the average sex composition, and the average balance between clinical and CST tests across the entire public testing data for the week. This adjustment allows more accurate comparison of the proportion testing positive across districts.

The report includes tests conducted between 1 March 2020 (week 10), the week when the first case of COVID-19 was confirmed, and 14 November 2020 (week 46).

Testing volumes and proportion testing positive

From 1 March through 14 November 2020, 4,354,676 laboratory tests for SARS-CoV-2 were performed. The number of tests performed increased to week 21, however decreased in weeks 22 and 23 due to a limited supply of extraction and testing kits. Increased volumes of tests were observed week on week from week 24 to week 28, with the highest number of tests performed in week 28 (n=272,592), but have subsequently decreased. In week 46, 103,231 tests were performed, similar to the number of tests performed in the previous few weeks. All tests for samples collected in the previous week may not yet be reflected. Reduced testing volumes were observed over weekends and public holidays (Figure 1).




Figure 1. Number of laboratory tests conducted by date of specimen collection, South Africa, 1 March – 14 November 2020. Blue dotted line shows the 7-day moving average of the number of tests conducted. Grey bars highlight weekend days and public holidays.

The overall percentage testing positive from week 10 through 46 was 16.6% (Table 1). The percentage testing

positive increased week on week from week 18 to a peak of 31.2% in week 29. Since week 29, there has been a

20.2% decrease in the percentage testing positive to 11.0% in week 46. The percentage testing positive in week

46 of 11.0% was slightly higher than observed in week 45 (10.3%, P<0.001) (Figure 2).

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Week number Week beginning No. of tests n (%) No. of positive tests Percentage testing positive (%)

10 01-Mar 410 (0.0) 9 2.2

11 08-Mar 2329 (0.1) 88 3.8

12 15-Mar 21317 (0.5) 825 3.9

13 22-Mar 17039 (0.4) 470 2.8

14 29-Mar 17382 (0.4) 399 2.3

15 05-Apr 24590 (0.6) 568 2.3

16 12-Apr 41857 (1.0) 1047 2.5

17 19-Apr 75869 (1.7) 1924 2.5

18 26-Apr 89477 (2.1) 2886 3.2

19 03-May 136862 (3.1) 5532 4.0

20 10-May 156993 (3.6) 7416 4.7

21 17-May 156371 (3.6) 10485 6.7

22 24-May 141897 (3.3) 11672 8.2

23 31-May 136124 (3.1) 13453 9.9

24 07-Jun 156768 (3.6) 20448 13.0

25 14-Jun 164979 (3.8) 29831 18.1

26 21-Jun 222079 (5.1) 50377 22.7

27 28-Jun 268910 (6.2) 69063 25.7

28 05-Jul 272592 (6.3) 79513 29.2

29 12-Jul 250197 (5.7) 78143 31.2

30 19-Jul 236130 (5.4) 72277 30.6

31 26-Jul 185516 (4.3) 53496 28.8

32 02-Aug 150398 (3.5) 36807 24.5

33 09-Aug 117333 (2.7) 23417 20.0

34 16-Aug 110112 (2.5) 19080 17.3

35 23-Aug 99947 (2.3) 14623 14.6

36 30-Aug 90405 (2.1) 11402 12.6

37 06-Sep 94092 (2.2) 10790 11.5

38 13-Sep 97533 (2.2) 10892 11.2

39 20-Sep 79194 (1.8) 9175 11.6

40 27-Sep 98163 (2.3) 10018 10.2

41 04-Oct 105055 (2.4) 10680 10.2

42 11-Oct 109365 (2.5) 11014 10.1

43 18-Oct 111939 (2.6) 11035 9.9

44 25-Oct 105604 (2.4) 10401 9.8

45 01-Nov 106617 (2.4) 10939 10.3

46 08-Nov 103231 (2.4) 11312 11.0

Total 4354676 (100.0) 721507 16.6

Table 1. Weekly number of tests conducted and positive tests, South Africa, 1 March – 14 November 2020




Figure 2. Percentage of laboratory tests positive for SARS-CoV-2 by date of specimen collection, South Africa, 1 March – 14 November 2020. Blue dotted line shows the 7-day moving average of the percentage testing positive. Grey bars highlight weekend days and public holidays.

Testing in private and public sectors

From 1 March through 14 November, 1,984,082 laboratory tests were conducted in public sector laboratories, with 15.5% testing positive. Over this same period, private sector laboratories conducted 2,370,594 tests, with 17.5% testing positive (Table 2). Overall the public sector has conducted 45.6% of tests and accounted for 42.5% of positive tests. The peak percentage testing positive was observed in week 30 in the public sector (29.5%), and in week 29 in the private sector (32.8%). From week 45 to week 46, the percentage testing positive increased from 11.9% to 12.8% (P<0.001) in the public sector and increased slightly from 9.0% to 9.6% (P<0.001) in the private sector. In week 46 the percentage testing positive

continued to be higher in the public sector (12.8%) compared to the private sector (9.6%) (P<0.001), as has been observed since week 34.

The mean turnaround time for tests conducted in week 46 was 1.4 days. Turnaround time was unchanged in the public sector (1.9 days) and decreased in the private sector (1.0 days) (Figure 3). Turnaround times for public sector tests were >2 days in Mpumalanga (2.8 days), Eastern Cape (2.7 days) and KwaZulu-Natal (2.1 days) (Figure 4). Turnaround times in the past week increased in Mpumalanga (2.0 to 2.8 days). Twenty-four of the 28 (85.7%) NHLS laboratories performing testing for SARS-CoV-2 had turnaround times ≤2 days (Figure 5).

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Public sector Private sector Public sector percentage of Ratio of PTPaWeek

numberWeek

beginning Tests Casesn (%) Tests Positive tests

n (%) Tests (%) Positive tests (%)

10 01-Mar 251 5 (2.0) 159 4 (2.5) 61.2 55.6 0.79211 08-Mar 350 12 (3.4) 1979 76 (3.8) 15.0 13.6 0.89312 15-Mar 1344 51 (3.8) 19973 774 (3.9) 6.3 6.2 0.97913 22-Mar 3357 124 (3.7) 13682 346 (2.5) 19.7 26.4 1.46114 29-Mar 5608 158 (2.8) 11774 241 (2.0) 32.3 39.6 1.37615 05-Apr 11320 319 (2.8) 13270 249 (1.9) 46.0 56.2 1.50216 12-Apr 23753 606 (2.6) 18104 441 (2.4) 56.7 57.9 1.04717 19-Apr 54130 1468 (2.7) 21739 456 (2.1) 71.3 76.3 1.29318 26-Apr 66178 2276 (3.4) 23299 610 (2.6) 74.0 78.9 1.31419 03-May 92280 4225 (4.6) 44582 1307 (2.9) 67.4 76.4 1.56220 10-May 104907 5075 (4.8) 52086 2341 (4.5) 66.8 68.4 1.07621 17-May 95409 6583 (6.9) 60962 3902 (6.4) 61.0 62.8 1.07822 24-May 74212 5922 (8.0) 67685 5750 (8.5) 52.3 50.7 0.93923 31-May 60207 6065 (10.1) 75917 7388 (9.7) 44.2 45.1 1.03524 07-Jun 59942 7312 (12.2) 96826 13136 (13.6) 38.2 35.8 0.89925 14-Jun 55948 11001 (19.7) 109031 18830 (17.3) 33.9 36.9 1.13926 21-Jun 82549 18768 (22.7) 139530 31609 (22.7) 37.2 37.3 1.00427 28-Jun 97230 25031 (25.7) 171680 44032 (25.6) 36.2 36.2 1.00428 05-Jul 107949 30198 (28.0) 164643 49315 (30.0) 39.6 38.0 0.93429 12-Jul 101259 29316 (29.0) 148938 48827 (32.8) 40.5 37.5 0.88330 19-Jul 96170 28334 (29.5) 139960 43943 (31.4) 40.7 39.2 0.93831 26-Jul 73896 21277 (28.8) 111620 32219 (28.9) 39.8 39.8 0.99832 02-Aug 64063 15708 (24.5) 86335 21099 (24.4) 42.6 42.7 1.00333 09-Aug 53650 10382 (19.4) 63683 13035 (20.5) 45.7 44.3 0.94534 16-Aug 50889 8911 (17.5) 59223 10169 (17.2) 46.2 46.7 1.02035 23-Aug 45472 7209 (15.9) 54475 7414 (13.6) 45.5 49.3 1.16536 30-Aug 41051 5596 (13.6) 49354 5806 (11.8) 45.4 49.1 1.15937 06-Sep 46370 5963 (12.9) 47722 4827 (10.1) 49.3 55.3 1.27138 13-Sep 49086 6085 (12.4) 48447 4807 (9.9) 50.3 55.9 1.24939 20-Sep 40924 5120 (12.5) 38270 4055 (10.6) 51.7 55.8 1.18140 27-Sep 44260 5203 (11.8) 53903 4815 (8.9) 45.1 51.9 1.31641 04-Oct 46361 5197 (11.2) 58694 5483 (9.3) 44.1 48.7 1.20042 11-Oct 48212 5296 (11.0) 61153 5718 (9.4) 44.1 48.1 1.17543 18-Oct 50182 5615 (11.2) 61757 5420 (8.8) 44.8 50.9 1.27544 25-Oct 45524 5316 (11.7) 60080 5085 (8.5) 43.1 51.1 1.38045 01-Nov 46518 5524 (11.9) 60099 5415 (9.0) 43.6 50.5 1.31846 08-Nov 43271 5540 (12.8) 59960 5772 (9.6) 41.9 49.0 1.330

Total 1984082 306791 (15.5) 2370594 414716 (17.5) 45.6 42.5 0.884

Table 2. Weekly number of tests conducted and positive tests, by healthcare sector, South Africa, 1 March – 14 November 2020

aRatio of percentage testing positive (PTP) in the public sector to the private sector calculated as (no. of cases/total tests in public sector)/ (no. of cases/total tests in private sector)




Figure 3. Mean number of days between date of specimen collection and date of test result, by week of test result, South Africa, 18 October – 14 November 2020

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Figure 4. Mean number of days between date of specimen collection and date of test result, by week of test result and province, public sector, South Africa, 18 October – 14 November 2020. WC, Western Cape; EC, Eastern Cape; FS, Free State; KZN, KwaZulu-Natal; GT, Gauteng; NC, Northern Cape; NW, North West; MP, Mpumalanga; LP, Limpopo

Figure 5. Mean number of days between date of specimen collection and date of test result, by public sector laboratory, 25 October – 14 November 2020. The horizontal black line indicates 48-hour turnaround time (TAT).

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WC EC NC FS KZN NW GT MP LP

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Testing by province

Gauteng (29.7%) performed the largest number of tests in week 46, followed by Western Cape (18.6%), Eastern Cape (16.1%) and KwaZulu-Natal (15.1%) provinces (Table 3). Western Cape (275 per 100,000 persons), Eastern Cape (248 per 100,000 persons), Northern Cape (233 per 100,000 persons) and Free State (230 per 100,000 persons) provinces had the highest testing rates in week 46 (Figure 6). Testing rates have decreased in all provinces since peak testing rates were observed between week 21 (Western Cape) and week 31 (Northern Cape) in the respective provinces. Testing rates increased in the Eastern Cape and Western Cape over recent weeks, and continued to decrease in Northern Cape and Free State.

The percentage testing positive in week 46 continued to be highest in the Eastern Cape (31.9%), followed by the Western Cape (12.2%). Percentages testing positive were <10% in Northern Cape, Free State, KwaZulu-Natal, North West, Gauteng, Mpumalanga and Limpopo in week 46 (Figure 7). Compared to the previous week, the percentage testing positive increased by 3.3% in the Western Cape (8.9% to 12.2%, P<0.001) and 2.7% in the Eastern Cape (29.2% to 31.9%, P<0.001) in week 46. The percentage testing positive in week 46 compared to week 45 decreased in Northern Cape (P=0.036), Free State (P<0.001) and Mpumalanga (P=0.004), and did not change in KwaZulu-Natal (P=0.123), North West (P=0.626), Gauteng (P=0.206) and Limpopo (P=0.705). The percentage testing positive was higher than the national average, not weighted for population size, in the Eastern Cape, and Western Cape provinces (Figure 7).

Figure 6. Testing rate per 100,000 persons by province and week of specimen collection, South Africa, 1 March – 14 November 2020

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Testing in the public sector

In the public sector, the percentage testing positive increased in the past week (11.9% in week 45 to 12.8% in week 46, P<0.001) (Table 4). The percentage testing positive in week 46 continued to be highest in the

Eastern Cape (29.6%), followed by North West (17.9%), Western Cape (15.8%) and Limpopo (13.1%) provinces. The percentage testing positive in the public sector remains higher than the national average, not weighted for population size, in the Western Cape, Eastern Cape, North West and Limpopo provinces (Figure 8).




25-31 Oct 1-7 Nov 8-14 Nov

Province Populationa No. of tests

No. positive tests (%)

No. of tests


No. of tests


Tests per 100,000 persons

Change in percentage

positiveb

Western Cape 7005741 16930 1349 (8.0) 18169 1616 (8.9) 19235 2349 (12.2) 275 3.3%Eastern Cape 6734001 13490 3325 (24.6) 17040 4972 (29.2) 16670 5321 (31.9) 248 2.7%Northern Cape 1292786 4032 600 (14.9) 3271 374 (11.4) 3009 295 (9.8) 233 -1.6%Free State 2928903 8371 1246 (14.9) 7240 769 (10.6) 6747 424 (6.3) 230 -4.3%KwaZulu-Natal 11531628 16903 878 (5.2) 17336 805 (4.6) 15614 782 (5.0) 135 0.4%North West 4108816 4378 556 (12.7) 3731 372 (10.0) 3695 356 (9.6) 90 -0.3%Gauteng 15488137 32927 1609 (4.9) 31473 1297 (4.1) 30700 1204 (3.9) 198 -0.2%Mpumalanga 4679786 5708 499 (8.7) 5670 487 (8.6) 5040 358 (7.1) 108 -1.5%Limpopo 5852553 2663 336 (12.6) 2504 244 (9.7) 2261 213 (9.4) 39 -0.3%Unknown 202 3 (1.5) 183 3 (1.6) 260 10 (3.8) 2.2%Total 59622350 105604 10401 (9.8) 106617 10939 (10.3) 103231 11312 (11.0) 173 0.7%

Table 3. Weekly number of tests performed and positive tests, by province, South Africa, 25 October – 14 November 2020

a 2020 Mid-year population Statistics SA

b Current week compared to previous week

Figure 7. Weekly percentage testing positive, by province, South Africa, 25 October – 14 November 2020. The horizontal blue line shows the national mean for week 46, beginning 8 November 2020.

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Figure 8. Weekly percentage testing positive in the public sector, by province, South Africa, 25 October – 14 November 2020. The horizontal blue line shows the national mean for week 46, beginning 8 November 2020.

Public facilities with high proportions testing positive

Table 5 shows the 25 public clinics, hospitals and testing laboratories (where specimens were not tied to a particular facility), that had 25 or more specimens

tested and at least five positive results in the week of 8-14 November, with the highest proportion testing positive nationally. This week’s list is dominated by facilities in the Eastern Cape (15) and Western Cape (9).




25-31 Oct 1-7 Nov 8-14 Nov

Province No. of tests No. positive tests (%) No. of tests No. positive

tests (%) No. of tests No. positive tests (%)

Western Cape 6420 552 (8.6) 7074 748 (10.6) 7517 1186 (15.8)Eastern Cape 8630 2002 (23.2) 10767 2819 (26.2) 9344 2766 (29.6)Northern Cape 2405 309 (12.8) 1870 197 (10.5) 1769 175 (9.9)Free State 4343 727 (16.7) 3684 398 (10.8) 2924 208 (7.1)KwaZulu-Natal 8755 467 (5.3) 9106 394 (4.3) 8035 344 (4.3)North West 1371 271 (19.8) 1247 200 (16.0) 1243 223 (17.9)Gauteng 10753 614 (5.7) 10003 440 (4.4) 9884 379 (3.8)Mpumalanga 1913 214 (11.2) 1853 207 (11.2) 1741 154 (8.8)Limpopo 934 160 (17.1) 914 121 (13.2) 792 104 (13.1)Unknown 0 0 (0.0) 0 0 (0.0) 22 1 (4.5)Total 45524 5316 (11.7) 46518 5524 (11.9) 43271 5540 (12.8)

Table 4. Weekly number of tests conducted and positive tests in the public sector, by province, South Africa, 25 October – 14

November 2020

PROVINCE

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Western Cape Eastern Cape Northern Cape Free State KwaZulu-Natal North West Gauteng Mpumalanga Limpopo

25-31 OCT 1-7 NOV 8-14 NOV

0%

5%

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35%

Public sector testing: Health district-level results

The results for the 25 municipalities and metropolitan health sub-districts showing the greatest proportions testing positive in the week of 8-14 November 2020 are shown in Table 6. Districts showing the greatest proportions testing positive are concentrated in the Eastern Cape (15 districts), with 4 in the Western Cape, and 3 in each of Limpopo and the North West.

Bitou recorded the highest proportion testing positive for the second week in a row. Three districts showed a proportion testing positive greater than 40%, 9 greater than 30% and 6 showed a proportion testing positive less than 25%. A significant increase over the week was observed in seven districts – George and Knysna in the Western Cape; Nelson Mandela Bay districts B and C, Mnquma, and Lukanji in the Eastern Cape; and Ramotshere Moiloa in the North West.




Facility Name Province Tests PTP (95% CI)Facility 1 Eastern Cape 37 0.730 (0.587;0.873)

Facility 2 Eastern Cape 80 0.600 (0.493;0.707)

Facility 3 North West 25 0.560 (0.365;0.755)


Facility 5 Western Cape 43 0.535 (0.386;0.684)



















Facility 24 Western Cape 118 0.424 (0.335;0.513)Facility 25 Eastern Cape 140 0.421 (0.340;0.503)

Table 5. Public healthcare facilities with a high proportion testing positive, 8-14 November 2020

95% CI: 95% confidence interval; PTP: positive test proportion

The data for every district with a non-zero proportion testing positive or where the range of confidence interval is not more than 30% (15% either side of the point estimate) for the current week is presented graphically below.




Health district or sub-district Province PTP (95% CI) Previous weekBitou Western Cape 0.434 (0.364-0.505) 0.380 (0.287-0.472)

George Western Cape 0.403 (0.369-0.436) 0.260 (0.224-0.295)

Knysna Western Cape 0.400 (0.350-0.450) 0.205 (0.158-0.251)

Nelson Mandela Bay B Eastern Cape 0.380 (0.356-0.403) 0.319 (0.297-0.341)

Ndlambe Eastern Cape 0.366 (0.298-0.435) 0.334 (0.282-0.385)

Nelson Mandela Bay C Eastern Cape 0.348 (0.328-0.367) 0.299 (0.282-0.316)

Nelson Mandela Bay A Eastern Cape 0.332 (0.287-0.376) 0.334 (0.301-0.366)

Mnquma Eastern Cape 0.323 (0.216-0.430) 0.091 (0.039-0.143)

Ngqushwa Eastern Cape 0.314 (0.220-0.409) 0.284 (0.204-0.364)

Makana Eastern Cape 0.312 (0.268-0.356) 0.310 (0.262-0.358)

Lukanji Eastern Cape 0.302 (0.195-0.409) 0.109 (0.057-0.161)

Kouga Eastern Cape 0.300 (0.257-0.343) 0.290 (0.245-0.336)

Mafikeng North West 0.277 (0.209-0.345) 0.238 (0.184-0.292)

Thulamela Limpopo 0.274 (0.150-0.397) 0.173 (0.087-0.259)

Makhado Limpopo 0.271 (0.144-0.398) 0.130 (0.033-0.227)

Senqu Eastern Cape 0.263 (0.127-0.399) 0.161 (0.096-0.226)

Amahlathi Eastern Cape 0.260 (0.174-0.347) 0.192 (0.136-0.249)

Ramotshere Moiloa North West 0.258 (0.180-0.336) 0.057 (0.016-0.098)

Sundays River Valley Eastern Cape 0.251 (0.180-0.322) 0.269 (0.211-0.327)

Baviaans Eastern Cape 0.246 (0.143-0.349) 0.246 (0.166-0.325)

Ikwezi Eastern Cape 0.235 (0.131-0.340) 0.213 (0.140-0.286)

Mossel Bay Western Cape 0.234 (0.187-0.281) 0.184 (0.127-0.241)

Camdeboo Eastern Cape 0.229 (0.197-0.261) 0.279 (0.235-0.323)

Makhuduthamaga Limpopo 0.215 (0.072-0.358) 0.089 (0.000-0.186)Tlokwe City Council North West 0.207 (0.091-0.322) 0.226 (0.130-0.321)

Table 6. Health sub-districts with the highest proportion testing positive based on public sector data for the week of 8-14 November 2020

95% CI: 95% confidence interval; PTP: adjusted positive test proportion; PTP marked in red or blue have current week proportions testing positive that are significantly higher or lower than the previous week, respectively.




Figure 9. Proportions testing positive by health sub-districts in Western Cape, Eastern Cape, Gauteng, KwaZulu-Natal, North West, Free State, Limpopo, Mpumalanga and Northern Cape provinces based on public sector data for the week of 8-14 November 2020.

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The spatial pattern of adjusted proportions testing positive in public facilities by health district and sub-district are shown for South Africa (Figure 10), Western Cape (Figure 11), Eastern Cape (Figure 12), Northern Cape (Figure 13), Free State (Figure 14), KwaZulu-Natal (Figure 15), North West (Figure 16), Gauteng (Figure 17), Mpumalanga (Figure 18) and Limpopo (Figure 19).

Figure 10. Proportion testing positive by health sub-district based on public sector data for the week of 8-14 November 2020, South Africa. Areas shaded white represent districts in which either (i) no tests were conducted, (ii) all tests were negative, or (iii) the confidence interval exceeded 30%.

Figure 11. Health sub-districts in the Western Cape province with a high proportion testing positive based on public sector data for the week of 8-14 November 2020. Areas shaded white represent districts in which either (i) no tests were conducted, (ii) all tests were negative, or (iii) the confidence interval exceeded 30%




Figure 12. Health sub-districts in the Eastern Cape province with a high proportion testing positive based on public sector data for the week of 8-14 November 2020. Areas shaded white represent districts in which either (i) no tests were conducted, (ii) all tests were negative, or (iii) the confidence interval exceeded 30%.

Figure 13. Health sub-districts in Northern Cape Province with a high proportion testing positive based on public sector data for the week of 8-14 November 2020. Areas shaded white represent districts in which either (i) no tests were conducted, (ii) all tests were negative, or (iii) the confidence interval exceeded 30%.




Figure 15. Health sub-districts in KwaZulu-Natal Province with a high proportion testing positive based on public sector data for the week of 8-14 November 2020. Areas shaded white represent districts in which either (i) no tests were conducted, (ii) all tests were negative, or (iii) the confidence interval exceeded 30%.

Figure 14. Health sub-districts in Free State Province with a high proportion testing positive based on public sector data for the week of 8-14 November 2020. Areas shaded white represent districts in which either (i) no tests were conducted, (ii) all tests were negative, or (iii) the confidence interval exceeded 30%.




Figure 17. Health sub-districts in Gauteng Province with a high proportion testing positive based on public sector data for the week of 8-14 November 2020. Areas shaded white represent districts in which either (i) no tests were conducted, (ii) all tests were negative, or (iii) the confidence interval exceeded 30%.

Figure 16. Health sub-districts in North West Province with a high proportion testing positive based on public sector data for the week of 8-14 November 2020. Areas shaded white represent districts in which either (i) no tests were conducted, (ii) all tests were negative, or (iii) the confidence interval exceeded 30%.




Figure 18. Health sub-districts in Mpumalanga Province with a high proportion testing positive based on public sector data for the week of 8-14 November 2020. Areas shaded white represent districts in which either (i) no tests were conducted, (ii) all tests were negative, or (iii) the confidence interval exceeded 30%.

Figure 19. Health sub-districts in Limpopo Province with a high proportion testing positive based on public sector data for the week of 8-14 November 2020. Areas shaded white represent districts in which either (i) no tests were conducted, (ii) all tests were negative, or (iii) the confidence interval exceeded 30%.







Figure 20. Percentage of inpatient tests performed in the public sector by province, 18 October – 14 November 2020

Figure 21. Percentage testing positive by patient admission status in the public sector, 18 October – 14 November 2020

Testing by patient admission status

In week 46, 34.2% of tests in the public sector were performed for hospitalised patients (Figure 20). The proportion of inpatient tests was highest in KwaZulu-Natal (46.4%), Gauteng (44.6%), Northern Cape (43.6%) and North West (42.3%) provinces. Comparing week 46 to the previous week, the proportion of inpatient tests increased in seven provinces including Eastern

Cape, Northern Cape, Free State, KwaZulu-Natal, North West, Gauteng and Limpopo. The percentage testing positive in week 46 remained lower among inpatients (8.5%) compared to outpatients (15.3%), although higher in both groups compared to the previous week (Figure 21). In the public sector in week 46 the mean laboratory turnaround time continued to be lower for inpatients (1.5 days) compared to outpatients (2.2 days) (Figure 22).

WESTERN CAPE EASTERN CAPE FREE STATE KWAZULU-NATAL

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Figure 22. Mean number of days between date of specimen collection and date of test result, by patient admission status and date of test result in the public sector, South Africa, 18 October – 14 November 2020

Mean age of tested (years) Mean age of positive tests (years)

Sex ratios (males / 100 females)

Week number

Week beginning Males Females Males Females Tested Positive tests

43 18 October 38.1 38.5 39.9 39.9 88.1 72.744 25 October 38.9 39.4 40.7 40.9 90.1 76.245 1 November 39.0 39.5 40.6 40.9 90.0 76.846 8 November 39.1 39.5 41.8 41.7 89.3 77.1

Table 7. Mean age and sex ratio of individuals tested, South Africa, 18 October – 14 November 2020

Testing by age and sex

The mean age of individuals tested in week 46 was 39.3 years, similar to the previous week. The mean age of individuals with a positive test in week 46 was 41.7 years. The mean age of individuals with a positive test in week 46 did not differ between males (41.8 years)

and females (41.7 years, P=0.703) (Table 7). The sex ratio (the number of males per 100 females) of individuals with a positive test in week 46 was 77.1. In both sexes the proportion testing positive in week 46 was similar to the previous two weeks in the younger age groups (<40 years), but increased in the older age groups (≥40 years) (Figure 23).

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Figure 23. Weekly proportion testing positive by age group and sex, South Africa, 25 October – 14 November 2020

Age (years) 18-24 Oct 25-31 Oct 1-7 Nov 8-14 NovMale Female Male Female Male Female Male Female

0-19 6.4% 7.8% 6.4% 7.9% 7.1% 8.3% 6.5% 7.7%

20-39 9.3% 11.0% 9.4% 10.2% 9.7% 10.8% 10.3% 11.4%

40-59 9.9% 12.6% 9.7% 13.3% 10.3% 13.3% 11.5% 14.3%

60-69 9.6% 11.3% 10.0% 10.9% 10.3% 11.5% 11.0% 13.6%

70+ 7.9% 8.6% 8.5% 8.2% 8.4% 8.4% 10.2% 9.4%

Total 8.9% 10.8% 9.0% 10.7% 9.4% 11.1% 10.2% 11.8%

Table 8. Percentage testing positive by sex and week, South Africa, 18 October – 14 November 2020

From week 43 to week 46, the percentage testing positive increased by 1.3% in males (from 8.9% to 10.2%) and increased by 1.0% in females (from 10.8% to 11.8%) (Table 8). In week 46 the percentage testing

positive was higher in females compared to males in the 0-19 years (P=0.003), 20-39 years (P<0.001), 40-59 years (P<0.001) and 60-69 years (P<0.001) age groups, and did not differ in individuals aged ≥70 years.

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0 - 9 10 - 19 20 - 29 30 - 39 40 - 49 50 - 59 60 - 69 70 -79 80+

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Limitations

• A backlog in testing of samples by laboratories affects the reported numbers of tests performed. As a result, numbers tested during this period may change in subsequent reports.

• If higher-priority specimens were tested preferentially, this would likely result in an inflated proportion testing positive.

• Different and changing testing strategies (targeted vs. mass testing) used by different provinces makes percentage testing positive difficult to interpret and compare.

• Health district and sub-district level results included public-sector data only and were mapped based on the testing facility and not place of residence.

• Patient admission status was categorised based on the reported patient facility, which was only available for public sector data and may not reflect whether the patient was actually admitted to hospital.

• Province was determined based on the location of the laboratory where the specimen was registered, which may have resulted in misallocation of tests if the sample was registered in a different province to the patient residence.

Weekly testing volumes peaked in week 28, and subsequently decreased. The number of tests performed in week 46 were similar to the previous few weeks. Gauteng (29.7%), Western Cape (18.6%), Eastern Cape (16.1%) and KwaZulu-Natal (15.1%) provinces performed the majority of tests in the past week. Western Cape (275 per 100,000 persons), Eastern Cape (248 per 100,000 persons), Northern Cape (233 per 100,000 persons) and Free State (230 per 100,000 persons) provinces had the highest testing rates in week 46, with increases in testing rates observed in Eastern Cape and Western Cape. The overall laboratory turnaround time in week 46 was 1.4 days; 1.9 days in the public sector and 1.0 day in the private sector.

The percentage testing positive has decreased from a peak of 31.2% in week 29. In week 46 the percentage testing positive was 11.0%, slightly higher than the previous six weeks. The percentage testing positive was highest in the Eastern Cape (31.9%) and Western Cape (12.2%). Percentages testing positive were <10% in Northern Cape, Free State, North West, Gauteng, KwaZulu-Natal, Mpumalanga and Limpopo. In week 46, compared to the previous week, the percentage testing positive increased in the Eastern Cape and Western Cape, decreased in Northern Cape, Free State, and Mpumalanga, and did not change in KwaZulu-Natal, North West, Gauteng and Limpopo. Of the 25 districts with the highest proportions testing positive in week 46, fifteen were in the Eastern Cape.

CONCLUSIONS

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